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Display OMOP CDM data into Atlas


#1

Dear OHDSI Community,
At first thank you a lot for all the hard work you are doing to provide such tools and his forums to help us!

I am a new member (even if I was reading your posts to help me in the implementation of OMOP CDM Data format) but I must recognize I am quite lost with the Atlas web interface.

Indeed, I have a PostgreSQL database fulfilled with OMOP data (transformed from Optum source files we got) in 5.3 version but within Atlas I am not able to display any of those data (for example the Person CDM data). Do we have to do a specific configuration/action within Atlas to make sure Atlas can display it to our end users?
Is it required to use Achilles R Package once the data is stored within the database to let Atlas able to display it?

Thank you very much in advance for ALL your inputs, it will be truly helpful.
Warm regards,
Arnaud


(Ambuj) #2

Hello Arnaud,

Yes, we need to have Achilles set up to generate summary statistics, please refer the link below:

http://www.ohdsi.org/web/wiki/doku.php?id=documentation:software:atlas:setup

Thanks
-Ambuj


#3

Hello Ambuj and thank you a lot for your reply!

I tried to qualify my data with Achilles bu when my Achilles docker image is running, i am facing the following error message:

There is no relation “results.achilles_result”. I fulfilled myu results schema thanks to the DLL provided by the WebAPI application within my PostgreSQL database.
I did not find any useful inputs/issues regarding that specific table. Where can I find it? Thank you a lot in advance for your help


(Ambuj) #4

Please verify the schema by browsing following url in broswer:

http://localhost:8080/WebAPI/ddl/results?dialect=postgresql

That will show you the DDL for scripts, please verify and ensure the result schema have read/write permissions.


#5

Hello,

I got the schema from that URL (webapi 2.7.1) and there is no achilles_results table. Instead, There is a heracles_results.

I have created manually that table and the docker R Achilles package is working but how can I apply my JSON files obtained to Atlas in order to let my end users able to use it? Thank you very much

Hope it helps.


#6

Hello,

In addition to my previous reply, i have created manually the table by copying the heel_results one and it seems to work but unfortunately, here is the new error i am facing =>

select cast(analysis_id as int) as analysis_id, cast(stratum_1 as varchar(255)) as stratum_1, cast(stratum_2 as varchar(255)) as stratum_2, cast(stratum_3 as varchar(255)) as stratum_3, cast(stratum_4 as varchar(255)) as stratum_4, cast(stratum_5 as varchar(255)) as stratum_5, cast(count_value as bigint) as count_value from
s_tmpach_7 union all select 2000007 as analysis_id,

‘ERROR: check log files’ as stratum_1, NULL as stratum_2, NULL as stratum_3, NULL as stratum_4, NULL as stratum_5, 6 as count_value

It indicates that the s_tmparch_7 table does not exist and it does not specify a particular schema?

Thank you very much for your times & inputs!


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